I actually wonder that if Zn is bound but not ion, probably it can influence geometry of the whole protein if I parametrize it as an ion. Probably I should fix Zn residue and amino acid residues which are bound to it. I think it is reasonable.
Best regards,
Andrew
13.01.10, 09:47, "Ross Walker" <ross.rosswalker.co.uk>:
> Hi Andrew,
>
> If you think the zinc is purely structural and not involved in the actual
> binding site then you can just model it as a 2+ ion. Put TER cards around it
> in the pdb. Call it something like residue name ZNS (for structural Zinc)
> and give it atom name ZN.
>
> Then fire up leap and do:
>
> edit ZNS
>
> This will create a new unit called ZNS.
>
> Draw in a single new atom and then highlight and edit it.
>
> Set the charge to +2, the name and type to ZN.
>
> Then
>
> savemol2 ZNS ZNS.mol2
>
> Quit Leap.
>
> Create an frcmod file with the contents:
>
> Zinc 2+ Params
> MASS
> Zn 65.38
>
> BOND
>
> ANGL
>
> DIHE
>
> NONB
> Zn 1.85 0.06
>
>
> Finally you can fire up leap:
>
> source leaprc.ff99SB
> ZNS = loadmol2 ZNS.mol2
> loadamberparams frcmod
> foo = loadpdb foo.pdb
>
> And your zinc should be recognized.
>
> The only other thing you might have to do is make sure the protonation state
> (HIS/HID/HIP, CYS/CYX etc) is correct for the residues surrounding the zinc
> so you don't get H's added very close to the zinc.
>
> Good luck,
> Ross
>
> > -----Original Message-----
> > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of Andrew Voronkov
> > Sent: Wednesday, January 13, 2010 2:11 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] How to avoid Zn parametrization?
> >
> > Dear Amber users,
> > I have a protein which has Zn atom, bound directly to four amino acids
> > (Tankyrase PARP domain, 2rf5 code in PDB bank).
> > I need to test the results of docking of small ligands by MD run by
> > evaluation of the stability of complexes. The binding site is far from
> > Zn atom. For now I have no time to make parametrization for Zn atom as
> > far as it seems to be rather advanced and time consuming. What options
> > do I have?
> > For example I haven't included Zinc in docking site while performing
> > docking. Can I maybe make CAP molecular dynamics only for the binding
> > site of the ligand.
> > Probably parametrize zinc as ion, or just cut out Zn atom and fix all
> > Zn-surrounding amino acids as in the X-ray structure?
> >
> >
> > Best regards,
> > Andrew
> >
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>
>
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Received on Thu Jan 14 2010 - 05:30:03 PST
